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GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution.

Suvorova IA, Korostelev YD, Gelfand MS - PLoS ONE (2015)

Bottom Line: We also analyze the divergon structure and preferred site positions relative to regulated genes in the FADR and HUTC subfamilies.A single site in a divergon usually regulates both operons and is approximately in the middle of the intergenic area.Double sites are either involved in the co-operative regulation of both operons and then are in the center of the intergenic area, or each site in the pair independently regulates its own operon and tends to be near it.

View Article: PubMed Central - PubMed

Affiliation: Research and Training Center on Bioinformatics, Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia.

ABSTRACT
The GNTR family of transcription factors (TFs) is a large group of proteins present in diverse bacteria and regulating various biological processes. Here we use the comparative genomics approach to reconstruct regulons and identify binding motifs of regulators from three subfamilies of the GNTR family, FADR, HUTC, and YTRA. Using these data, we attempt to predict DNA-protein contacts by analyzing correlations between binding motifs in DNA and amino acid sequences of TFs. We identify pairs of positions with high correlation between amino acids and nucleotides for FADR, HUTC, and YTRA subfamilies and show that the most predicted DNA-protein interactions are quite similar in all subfamilies and conform well to the experimentally identified contacts formed by FadR from E. coli and AraR from B. subtilis. The most frequent predicted contacts in the analyzed subfamilies are Arg-G, Asn-A, Asp-C. We also analyze the divergon structure and preferred site positions relative to regulated genes in the FADR and HUTC subfamilies. A single site in a divergon usually regulates both operons and is approximately in the middle of the intergenic area. Double sites are either involved in the co-operative regulation of both operons and then are in the center of the intergenic area, or each site in the pair independently regulates its own operon and tends to be near it. We also identify additional candidate TF-binding boxes near palindromic binding sites of TFs from the FADR, HUTC, and YTRA subfamilies, which may play role in the binding of additional TF-subunits.

No MeSH data available.


Related in: MedlinePlus

Distribution of Snear and Srandom in the FadR, HutC and YtrA subfamilies.The vertical axis—the number of S values falling in the given interval. The horizontal axis—intervals of S values. Blue color denotes Snear values; red color—Srandom values. FadR subfamily data is shown in continuous lines; HutC subfamily, in dotted lines; YtrA subfamily, in dashed lines.
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pone.0132618.g010: Distribution of Snear and Srandom in the FadR, HutC and YtrA subfamilies.The vertical axis—the number of S values falling in the given interval. The horizontal axis—intervals of S values. Blue color denotes Snear values; red color—Srandom values. FadR subfamily data is shown in continuous lines; HutC subfamily, in dotted lines; YtrA subfamily, in dashed lines.

Mentions: The distributions of Snear and Srandom (Fig 10) were significantly different for all three subfamilies, FadR, HutC, and YtrA (the Wilcoxon rank-sum test, p<0.001). Moreover, the average Wnear value approximately equals half of the average Wtrue value, while average Wrandom value is close to zero, confirming that the used control is correct. These boxes may play a role in the regulation, though their exact function should be a subject of further experimental study.


GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution.

Suvorova IA, Korostelev YD, Gelfand MS - PLoS ONE (2015)

Distribution of Snear and Srandom in the FadR, HutC and YtrA subfamilies.The vertical axis—the number of S values falling in the given interval. The horizontal axis—intervals of S values. Blue color denotes Snear values; red color—Srandom values. FadR subfamily data is shown in continuous lines; HutC subfamily, in dotted lines; YtrA subfamily, in dashed lines.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494728&req=5

pone.0132618.g010: Distribution of Snear and Srandom in the FadR, HutC and YtrA subfamilies.The vertical axis—the number of S values falling in the given interval. The horizontal axis—intervals of S values. Blue color denotes Snear values; red color—Srandom values. FadR subfamily data is shown in continuous lines; HutC subfamily, in dotted lines; YtrA subfamily, in dashed lines.
Mentions: The distributions of Snear and Srandom (Fig 10) were significantly different for all three subfamilies, FadR, HutC, and YtrA (the Wilcoxon rank-sum test, p<0.001). Moreover, the average Wnear value approximately equals half of the average Wtrue value, while average Wrandom value is close to zero, confirming that the used control is correct. These boxes may play a role in the regulation, though their exact function should be a subject of further experimental study.

Bottom Line: We also analyze the divergon structure and preferred site positions relative to regulated genes in the FADR and HUTC subfamilies.A single site in a divergon usually regulates both operons and is approximately in the middle of the intergenic area.Double sites are either involved in the co-operative regulation of both operons and then are in the center of the intergenic area, or each site in the pair independently regulates its own operon and tends to be near it.

View Article: PubMed Central - PubMed

Affiliation: Research and Training Center on Bioinformatics, Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia.

ABSTRACT
The GNTR family of transcription factors (TFs) is a large group of proteins present in diverse bacteria and regulating various biological processes. Here we use the comparative genomics approach to reconstruct regulons and identify binding motifs of regulators from three subfamilies of the GNTR family, FADR, HUTC, and YTRA. Using these data, we attempt to predict DNA-protein contacts by analyzing correlations between binding motifs in DNA and amino acid sequences of TFs. We identify pairs of positions with high correlation between amino acids and nucleotides for FADR, HUTC, and YTRA subfamilies and show that the most predicted DNA-protein interactions are quite similar in all subfamilies and conform well to the experimentally identified contacts formed by FadR from E. coli and AraR from B. subtilis. The most frequent predicted contacts in the analyzed subfamilies are Arg-G, Asn-A, Asp-C. We also analyze the divergon structure and preferred site positions relative to regulated genes in the FADR and HUTC subfamilies. A single site in a divergon usually regulates both operons and is approximately in the middle of the intergenic area. Double sites are either involved in the co-operative regulation of both operons and then are in the center of the intergenic area, or each site in the pair independently regulates its own operon and tends to be near it. We also identify additional candidate TF-binding boxes near palindromic binding sites of TFs from the FADR, HUTC, and YTRA subfamilies, which may play role in the binding of additional TF-subunits.

No MeSH data available.


Related in: MedlinePlus